X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=a88aa4a4ee30b6e5ea5920c84140c92bd5af46dc;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=af1ff7a4d87d4bb2bff91b5ef1f7b662263b4926;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index af1ff7a..a88aa4a 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -1,29 +1,37 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.gui; import java.awt.*; import java.awt.event.*; +import java.awt.font.LineMetrics; +import java.awt.geom.AffineTransform; import java.awt.image.*; +import java.util.Hashtable; + import javax.swing.*; +import com.stevesoft.pat.Regex; + +import jalview.analysis.AAFrequency; +import jalview.analysis.StructureFrequency; import jalview.datamodel.*; +import jalview.schemes.ColourSchemeI; /** * DOCUMENT ME! @@ -38,6 +46,11 @@ public class AnnotationPanel extends JPanel implements MouseListener, final String SHEET = "Sheet"; + /** + * For RNA secondary structure "stems" aka helices + */ + final String STEM = "RNA Helix"; + final String LABEL = "Label"; final String REMOVE = "Remove Annotation"; @@ -48,6 +61,8 @@ public class AnnotationPanel extends JPanel implements MouseListener, final Color SHEET_COLOUR = Color.green.darker().darker(); + final Color STEM_COLOUR = Color.blue.darker(); + /** DOCUMENT ME!! */ AlignViewport av; @@ -80,11 +95,16 @@ public class AnnotationPanel extends JPanel implements MouseListener, boolean MAC = false; + // for editing cursor + int cursorX = 0; + + int cursorY = 0; + /** * Creates a new AnnotationPanel object. * * @param ap - * DOCUMENT ME! + * DOCUMENT ME! */ public AnnotationPanel(AlignmentPanel ap) { @@ -112,7 +132,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void adjustmentValueChanged(AdjustmentEvent evt) { @@ -120,10 +140,32 @@ public class AnnotationPanel extends JPanel implements MouseListener, } /** - * DOCUMENT ME! + * Calculates the height of the annotation displayed in the annotation panel. + * Callers should normally call the ap.adjustAnnotationHeight method to ensure + * all annotation associated components are updated correctly. + * */ public int adjustPanelHeight() { + int height = calcPanelHeight(); + this.setPreferredSize(new Dimension(1, height)); + if (ap != null) + { + // revalidate only when the alignment panel is fully constructed + ap.validate(); + } + + return height; + } + + /** + * calculate the height for visible annotation, revalidating bounds where + * necessary ABSTRACT GUI METHOD + * + * @return total height of annotation + */ + public int calcPanelHeight() + { // setHeight of panels AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); int height = 0; @@ -132,6 +174,11 @@ public class AnnotationPanel extends JPanel implements MouseListener, { for (int i = 0; i < aa.length; i++) { + if (aa[i] == null) + { + System.err.println("Null annotation row: ignoring."); + continue; + } if (!aa[i].visible) { continue; @@ -162,13 +209,11 @@ public class AnnotationPanel extends JPanel implements MouseListener, height += aa[i].height; } } - else + if (height == 0) { + // set minimum height = 20; } - - this.setPreferredSize(new Dimension(1, height)); - return height; } @@ -176,11 +221,15 @@ public class AnnotationPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void actionPerformed(ActionEvent evt) { AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + if (aa == null) + { + return; + } Annotation[] anot = aa[activeRow].annotations; if (anot.length < av.getColumnSelection().getMax()) @@ -224,9 +273,9 @@ public class AnnotationPanel extends JPanel implements MouseListener, if (anot[index] == null) { anot[index] = new Annotation(label, "", ' ', 0); // TODO: verify that - // null exceptions - // aren't raised - // elsewhere. + // null exceptions + // aren't raised + // elsewhere. } else { @@ -270,6 +319,13 @@ public class AnnotationPanel extends JPanel implements MouseListener, symbol = "\u03B2"; } + // Added by LML to color stems + else if (evt.getActionCommand().equals(STEM)) + { + type = 'S'; + symbol = "\u03C3"; + } + if (!aa[activeRow].hasIcons) { aa[activeRow].hasIcons = true; @@ -324,14 +380,15 @@ public class AnnotationPanel extends JPanel implements MouseListener, continue; String tlabel = null; if (anot[index] != null) - { + { // LML added stem code if (label2.equals(HELIX) || label2.equals(SHEET) - || label2.equals(LABEL)) + || label2.equals(STEM) || label2.equals(LABEL)) { tlabel = anot[index].description; - if (tlabel == null) + if (tlabel == null || tlabel.length() < 1) { - if (label2.equals(HELIX) || label2.equals(SHEET)) + if (label2.equals(HELIX) || label2.equals(SHEET) + || label2.equals(STEM)) { tlabel = "" + anot[index].secondaryStructure; } @@ -358,7 +415,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mousePressed(MouseEvent evt) { @@ -404,12 +461,25 @@ public class AnnotationPanel extends JPanel implements MouseListener, } JPopupMenu pop = new JPopupMenu("Structure type"); - JMenuItem item = new JMenuItem(HELIX); - item.addActionListener(this); - pop.add(item); - item = new JMenuItem(SHEET); - item.addActionListener(this); - pop.add(item); + JMenuItem item; + /* + * Just display the needed structure options + */ + if (av.alignment.isNucleotide() == true) + { + item = new JMenuItem(STEM); + item.addActionListener(this); + pop.add(item); + } + else + { + item = new JMenuItem(HELIX); + item.addActionListener(this); + pop.add(item); + item = new JMenuItem(SHEET); + item.addActionListener(this); + pop.add(item); + } item = new JMenuItem(LABEL); item.addActionListener(this); pop.add(item); @@ -437,7 +507,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseReleased(MouseEvent evt) { @@ -451,7 +521,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseEntered(MouseEvent evt) { @@ -462,7 +532,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseExited(MouseEvent evt) { @@ -473,7 +543,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseDragged(MouseEvent evt) { @@ -499,7 +569,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseMoved(MouseEvent evt) { @@ -542,7 +612,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, res = av.getColumnSelection().adjustForHiddenColumns(res); } - if (aa[row].annotations != null && row > -1 + if (row > -1 && aa[row].annotations != null && res < (int) aa[row].annotations.length) { if (aa[row].graphGroup > -1) @@ -564,10 +634,16 @@ public class AnnotationPanel extends JPanel implements MouseListener, } } else if (aa[row].annotations[res] != null - && aa[row].annotations[res].description != null) + && aa[row].annotations[res].description != null + && aa[row].annotations[res].description.length() > 0) { this.setToolTipText(aa[row].annotations[res].description); } + else + { + // clear the tooltip. + this.setToolTipText(null); + } if (aa[row].annotations[res] != null) { @@ -592,17 +668,49 @@ public class AnnotationPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseClicked(MouseEvent evt) { + if (activeRow != -1) + { + AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation anot = aa[activeRow]; + + if (anot.description.equals("secondary structure")) + { + // System.out.println(anot.description+" "+anot.getRNAStruc()); + } + } + } + + // TODO mouseClicked-content and drawCursor are quite experimental! + public void drawCursor(Graphics graphics, SequenceI seq, int res, int x1, + int y1) + { + int pady = av.charHeight / 5; + int charOffset = 0; + graphics.setColor(Color.black); + graphics.fillRect(x1, y1, av.charWidth, av.charHeight); + + if (av.validCharWidth) + { + graphics.setColor(Color.white); + + char s = seq.getCharAt(res); + + charOffset = (av.charWidth - fm.charWidth(s)) / 2; + graphics.drawString(String.valueOf(s), charOffset + x1, + (y1 + av.charHeight) - pady); + } + } /** * DOCUMENT ME! * * @param g - * DOCUMENT ME! + * DOCUMENT ME! */ public void paintComponent(Graphics g) { @@ -649,7 +757,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, * non-Thread safe repaint * * @param horizontal - * repaint with horizontal shift in alignment + * repaint with horizontal shift in alignment */ public void fastPaint(int horizontal) { @@ -693,11 +801,11 @@ public class AnnotationPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param g - * DOCUMENT ME! + * DOCUMENT ME! * @param startRes - * DOCUMENT ME! + * DOCUMENT ME! * @param endRes - * DOCUMENT ME! + * DOCUMENT ME! */ public void drawComponent(Graphics g, int startRes, int endRes) { @@ -765,8 +873,15 @@ public class AnnotationPanel extends JPanel implements MouseListener, int iconOffset = 0; boolean validRes = false; boolean validEnd = false; + boolean labelAllCols = false; + boolean centreColLabels, centreColLabelsDef = av + .getCentreColumnLabels(); + boolean scaleColLabel = false; boolean[] graphGroupDrawn = new boolean[aa.length]; - + int charOffset = 0; // offset for a label + float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a + // column. + Font ofont = g.getFont(); // \u03B2 \u03B1 for (int i = 0; i < aa.length; i++) { @@ -776,10 +891,11 @@ public class AnnotationPanel extends JPanel implements MouseListener, { continue; } - + centreColLabels = row.centreColLabels || centreColLabelsDef; + labelAllCols = row.showAllColLabels; + scaleColLabel = row.scaleColLabel; lastSS = ' '; lastSSX = 0; - if (row.graph > 0) { if (row.graphGroup > -1 && graphGroupDrawn[row.graphGroup]) @@ -842,7 +958,9 @@ public class AnnotationPanel extends JPanel implements MouseListener, continue; } - x = 0; + // first pass sets up state for drawing continuation from left-hand column + // of startRes + x = (startRes == 0) ? 0 : -1; while (x < endRes - startRes) { if (av.hasHiddenColumns) @@ -868,139 +986,144 @@ public class AnnotationPanel extends JPanel implements MouseListener, { validRes = true; } - - if (activeRow == i) + if (x > -1) { - g.setColor(Color.red); - - if (av.getColumnSelection() != null) + if (activeRow == i) { - for (int n = 0; n < av.getColumnSelection().size(); n++) - { - int v = av.getColumnSelection().columnAt(n); + g.setColor(Color.red); - if (v == column) + if (av.getColumnSelection() != null) + { + for (int n = 0; n < av.getColumnSelection().size(); n++) { - g - .fillRect(x * av.charWidth, y, av.charWidth, - av.charHeight); + int v = av.getColumnSelection().columnAt(n); + + if (v == column) + { + g.fillRect(x * av.charWidth, y, av.charWidth, + av.charHeight); + } } } } - } - if (av.validCharWidth && validRes - && row.annotations[column].displayCharacter != null - && (row.annotations[column].displayCharacter.length() > 0)) - { + if (av.validCharWidth + && validRes + && row.annotations[column].displayCharacter != null + && (row.annotations[column].displayCharacter.length() > 0)) + { - int charOffset = (av.getCentreColumnLabels()) ? ((av.charWidth - fm - .charsWidth(row.annotations[column].displayCharacter - .toCharArray(), 0, - row.annotations[column].displayCharacter.length())) / 2) - : (av.charWidth - fm - .charWidth(row.annotations[column].displayCharacter - .charAt(0))) / 2; + if (centreColLabels || scaleColLabel) + { + fmWidth = (float) fm.charsWidth( + row.annotations[column].displayCharacter + .toCharArray(), 0, + row.annotations[column].displayCharacter.length()); - if (row.annotations[column].colour == null) - g.setColor(Color.black); - else - g.setColor(row.annotations[column].colour); + if (scaleColLabel) + { + // justify the label and scale to fit in column + if (fmWidth > av.charWidth) + { + // scale only if the current font isn't already small enough + fmScaling = av.charWidth; + fmScaling /= fmWidth; + g.setFont(ofont.deriveFont(AffineTransform + .getScaleInstance(fmScaling, 1.0))); + // and update the label's width to reflect the scaling. + fmWidth = av.charWidth; + } + } + } + else + { + fmWidth = (float) fm + .charWidth(row.annotations[column].displayCharacter + .charAt(0)); + } + charOffset = (int) ((av.charWidth - fmWidth) / 2f); - if (column == 0 || row.graph > 0) - { - g.drawString(row.annotations[column].displayCharacter, - (x * av.charWidth) + charOffset, y + iconOffset); - } - else if (row.annotations[column - 1] == null - || (!row.annotations[column].displayCharacter - .equals(row.annotations[column - 1].displayCharacter) || (row.annotations[column].displayCharacter - .length() < 2 && row.annotations[column].secondaryStructure == ' '))) - { - g.drawString(row.annotations[column].displayCharacter, x - * av.charWidth + charOffset, y + iconOffset); + if (row.annotations[column].colour == null) + g.setColor(Color.black); + else + g.setColor(row.annotations[column].colour); + + if (column == 0 || row.graph > 0) + { + g.drawString(row.annotations[column].displayCharacter, + (x * av.charWidth) + charOffset, y + iconOffset); + } + else if (row.annotations[column - 1] == null + || (labelAllCols + || !row.annotations[column].displayCharacter + .equals(row.annotations[column - 1].displayCharacter) || (row.annotations[column].displayCharacter + .length() < 2 && row.annotations[column].secondaryStructure == ' '))) + { + g.drawString(row.annotations[column].displayCharacter, x + * av.charWidth + charOffset, y + iconOffset); + } + g.setFont(ofont); } } - if (row.hasIcons) { - if (!validRes - || (row.annotations[column].secondaryStructure != lastSS)) + char ss = validRes ? row.annotations[column].secondaryStructure + : ' '; + if (ss == 'S') + { + // distinguish between forward/backward base-pairing + if (row.annotations[column].displayCharacter.indexOf(')') > -1) + { + ss = 's'; + } + } + if (!validRes || (ss != lastSS)) { - switch (lastSS) + if (x > -1) { - case 'H': - g.setColor(HELIX_COLOUR); - if (MAC) + switch (lastSS) { - // Off by 1 offset when drawing rects and ovals - // to offscreen image on the MAC - g.fillRoundRect(lastSSX, y + 4 + iconOffset, - (x * av.charWidth) - lastSSX, 7, 8, 8); + case 'H': + drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes, + column, validRes, validEnd); break; - } - - int sCol = (lastSSX / av.charWidth) + startRes; - int x1 = lastSSX; - int x2 = (x * av.charWidth); - - if (sCol == 0 - || row.annotations[sCol - 1] == null - || row.annotations[sCol - 1].secondaryStructure != 'H') - { - g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90, - 180); - x1 += av.charWidth / 2; - } - - if (row.annotations[column] == null - || row.annotations[column].secondaryStructure != 'H') - { - g.fillArc((x * av.charWidth) - av.charWidth, y + 4 - + iconOffset, av.charWidth, 8, 270, 180); - x2 -= av.charWidth / 2; - } - g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8); - break; - - case 'E': - g.setColor(SHEET_COLOUR); - g.fillRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth) - - lastSSX - 4, 7); - g.fillPolygon(new int[] - { (x * av.charWidth) - 4, (x * av.charWidth) - 4, - (x * av.charWidth) }, new int[] - { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, - 3); + case 'E': + drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes, + column, validRes, validEnd); + break; - break; + case 'S': // Stem case for RNA secondary structure + case 's': // and opposite direction + drawStemAnnot(g, row, lastSSX, x, y, iconOffset, startRes, + column, validRes, validEnd); + break; - default: - g.setColor(Color.gray); - g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth) - - lastSSX, 2); + default: + g.setColor(Color.gray); + g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth) + - lastSSX, 2); - break; + break; + } } - if (validRes) { - lastSS = row.annotations[column].secondaryStructure; + lastSS = ss; } else { lastSS = ' '; } - - lastSSX = (x * av.charWidth); + if (x > -1) + { + lastSSX = (x * av.charWidth); + } } } - column++; x++; } - if (column >= row.annotations.length) { column = row.annotations.length - 1; @@ -1018,66 +1141,22 @@ public class AnnotationPanel extends JPanel implements MouseListener, switch (lastSS) { case 'H': - g.setColor(HELIX_COLOUR); - if (MAC) - { - // Off by 1 offset when drawing rects and ovals - // to offscreen image on the MAC - g.fillRoundRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth) - - lastSSX, 7, 8, 8); - break; - } - - int sCol = (lastSSX / av.charWidth) + startRes; - int x1 = lastSSX; - int x2 = (x * av.charWidth); - - if (sCol == 0 || row.annotations[sCol - 1] == null - || row.annotations[sCol - 1].secondaryStructure != 'H') - { - g - .fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, - 90, 180); - x1 += av.charWidth / 2; - } - - if (row.annotations[column] == null - || row.annotations[column].secondaryStructure != 'H') - { - g.fillArc((x * av.charWidth) - av.charWidth, - y + 4 + iconOffset, av.charWidth, 8, 270, 180); - x2 -= av.charWidth / 2; - } - - g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8); - + drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes, + column, validRes, validEnd); break; case 'E': - g.setColor(SHEET_COLOUR); - - if (!validEnd || row.annotations[endRes] == null - || row.annotations[endRes].secondaryStructure != 'E') - { - g.fillRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth) - - lastSSX - 4, 7); - g.fillPolygon(new int[] - { (x * av.charWidth) - 4, (x * av.charWidth) - 4, - (x * av.charWidth) }, new int[] - { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset }, 3); - } - else - { - g.fillRect(lastSSX, y + 4 + iconOffset, (x + 1) * av.charWidth - - lastSSX, 7); - } + drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes, + column, validRes, validEnd); + break; + case 's': + case 'S': // Stem case for RNA secondary structure + drawStemAnnot(g, row, lastSSX, x, y, iconOffset, startRes, + column, validRes, validEnd); break; - default: - g.setColor(Color.gray); - g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth) - - lastSSX, 2); - + drawGlyphLine(g, row, lastSSX, x, y, iconOffset, startRes, + column, validRes, validEnd); break; } } @@ -1147,6 +1226,157 @@ public class AnnotationPanel extends JPanel implements MouseListener, } } + private void drawStemAnnot(Graphics g, AlignmentAnnotation row, + int lastSSX, int x, int y, int iconOffset, int startRes, + int column, boolean validRes, boolean validEnd) + { + g.setColor(STEM_COLOUR); + int sCol = (lastSSX / av.charWidth) + startRes; + int x1 = lastSSX; + int x2 = (x * av.charWidth); + Regex closeparen = new Regex("(\\))"); + + String dc = column == 0 ? "" + : row.annotations[column - 1].displayCharacter; + + boolean diffupstream = sCol == 0 || row.annotations[sCol - 1] == null + || !dc.equals(row.annotations[sCol - 1].displayCharacter); + boolean diffdownstream = !validRes || !validEnd + || row.annotations[column] == null + || !dc.equals(row.annotations[column].displayCharacter); + // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream); + // If a closing base pair half of the stem, display a backward arrow + if (column > 0 && closeparen.search(dc)) + { + if (diffupstream) + // if (validRes && column>1 && row.annotations[column-2]!=null && + // dc.equals(row.annotations[column-2].displayCharacter)) + { + g.fillPolygon(new int[] + { lastSSX + 5, lastSSX + 5, lastSSX }, new int[] + { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3); + x1 += 5; + } + if (diffdownstream) + { + x2 -= 1; + } + } + else + { + // display a forward arrow + if (diffdownstream) + { + g.fillPolygon(new int[] + { x2 - 5, x2 - 5, x2 }, new int[] + { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3); + x2 -= 5; + } + if (diffupstream) + { + x1 += 1; + } + } + // draw arrow body + g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7); + } + + private void drawGlyphLine(Graphics g, AlignmentAnnotation row, + int lastSSX, int x, int y, int iconOffset, int startRes, + int column, boolean validRes, boolean validEnd) + { + g.setColor(Color.gray); + g + .fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth) + - lastSSX, 2); + } + + private void drawSheetAnnot(Graphics g, AlignmentAnnotation row, + int lastSSX, int x, int y, int iconOffset, int startRes, + int column, boolean validRes, boolean validEnd) + { + g.setColor(SHEET_COLOUR); + + if (!validEnd || !validRes || row.annotations[column] == null + || row.annotations[column].secondaryStructure != 'E') + { + g.fillRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth) - lastSSX + - 4, 7); + g.fillPolygon( + new int[] + { (x * av.charWidth) - 4, (x * av.charWidth) - 4, + (x * av.charWidth) }, new int[] + { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset }, + 3); + } + else + { + g.fillRect(lastSSX, y + 4 + iconOffset, (x + 1) * av.charWidth + - lastSSX, 7); + } + + } + + private void drawHelixAnnot(Graphics g, AlignmentAnnotation row, + int lastSSX, int x, int y, int iconOffset, int startRes, + int column, boolean validRes, boolean validEnd) + { + g.setColor(HELIX_COLOUR); + + int sCol = (lastSSX / av.charWidth) + startRes; + int x1 = lastSSX; + int x2 = (x * av.charWidth); + + if (MAC) + { + int ofs = av.charWidth / 2; + // Off by 1 offset when drawing rects and ovals + // to offscreen image on the MAC + g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8); + if (sCol == 0 || row.annotations[sCol - 1] == null + || row.annotations[sCol - 1].secondaryStructure != 'H') + { + } + else + { + // g.setColor(Color.orange); + g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8, + 0, 0); + } + if (!validRes || row.annotations[column] == null + || row.annotations[column].secondaryStructure != 'H') + { + + } + else + { + // g.setColor(Color.magenta); + g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset, x2 - x1 - ofs + + 1, 8, 0, 0); + + } + + return; + } + + if (sCol == 0 || row.annotations[sCol - 1] == null + || row.annotations[sCol - 1].secondaryStructure != 'H') + { + g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90, 180); + x1 += av.charWidth / 2; + } + + if (!validRes || row.annotations[column] == null + || row.annotations[column].secondaryStructure != 'H') + { + g.fillArc((x * av.charWidth) - av.charWidth, y + 4 + iconOffset, + av.charWidth, 8, 270, 180); + x2 -= av.charWidth / 2; + } + + g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8); + } + public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes, int eRes, int y, float min, float max, int graphHeight) { @@ -1239,11 +1469,16 @@ public class AnnotationPanel extends JPanel implements MouseListener, public void drawBarGraph(Graphics g, AlignmentAnnotation aa, int sRes, int eRes, float min, float max, int y) { + ColourSchemeI profcolour = av.getGlobalColourScheme(); + if (profcolour == null) + { + profcolour = new jalview.schemes.ZappoColourScheme(); + } if (sRes > aa.annotations.length) { return; } - + Font ofont = g.getFont(); eRes = Math.min(eRes, aa.annotations.length); int x = 0, y1 = y, y2 = y; @@ -1261,7 +1496,21 @@ public class AnnotationPanel extends JPanel implements MouseListener, int column; int aaMax = aa.annotations.length - 1; - + boolean renderHistogram = true, renderProfile = true; + if (aa.autoCalculated && aa.label.startsWith("Consensus")) + { + // TODO: generalise this to have render styles for consensus/profile data + if (aa.groupRef != null) + { + renderHistogram = aa.groupRef.isShowConsensusHistogram(); + renderProfile = aa.groupRef.isShowSequenceLogo(); + } + else + { + renderHistogram = av.isShowConsensusHistogram(); + renderProfile = av.isShowSequenceLogo(); + } + } while (x < eRes - sRes) { column = sRes + x; @@ -1280,7 +1529,6 @@ public class AnnotationPanel extends JPanel implements MouseListener, x++; continue; } - if (aa.annotations[column].colour == null) g.setColor(Color.black); else @@ -1289,17 +1537,93 @@ public class AnnotationPanel extends JPanel implements MouseListener, y1 = y - (int) (((aa.annotations[column].value - min) / (range)) * aa.graphHeight); - if (y1 - y2 > 0) + if (renderHistogram) { - g.fillRect(x * av.charWidth, y2, av.charWidth, y1 - y2); + if (y1 - y2 > 0) + { + g.fillRect(x * av.charWidth, y2, av.charWidth, y1 - y2); + } + else + { + g.fillRect(x * av.charWidth, y1, av.charWidth, y2 - y1); + } } - else + // draw profile if available + if (renderProfile && aa.annotations[column].value != 0) { - g.fillRect(x * av.charWidth, y1, av.charWidth, y2 - y1); - } - x++; + int profl[] = getProfileFor(aa, column); + // just try to draw the logo if profl is not null + if (profl != null) + { + + int ht = y1, htn = y2 - y1;// aa.graphHeight; + float wdth; + double ht2 = 0; + char[] dc; + + /** + * profl.length == 51 indicates that the profile of a secondary + * structure conservation row was accesed. + * Therefore dc gets length 2, to have space for a basepair instead of + * just a single nucleotide + */ + if (profl.length == 51) + { + dc = new char[2]; + } + else + { + dc = new char[1]; + } + + LineMetrics lm; + for (int c = 1; profl != null && c < profl[0];) + { + dc[0] = (char) profl[c++]; + + if (aa.label.startsWith("StrucConsensus")) + { + dc[1] = (char) profl[c++]; + } + + wdth = av.charWidth; + wdth /= (float) fm.charsWidth(dc, 0, dc.length); + if (c > 2) + { + ht += (int) ht2; + } + { + // if (aa.annotations[column].value==0) { + // g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(wdth, + // (ht2=(aa.graphHeight*0.1/av.charHeight))))); + // ht = y2-(int)ht2; + // } else { + g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance( + wdth, (ht2 = (htn * ((double) profl[c++]) / 100.0)) + / av.charHeight))); + lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g); + // htn -=ht2; + // } + g.setColor(profcolour.findColour(dc[0])); // (av.globalColourScheme!=null) + // ? );// try to get a + // colourscheme for the + // group(aa.groupRef.cs==null) + // ? av.textColour2 : + // cs.findColour(dc)); + // System.out.println(dc[0]); + + g.drawChars(dc, 0, dc.length, x * av.charWidth, + (int) (ht + lm.getHeight())); + + // ht+=g.getFontMetrics().getAscent()-g.getFontMetrics().getDescent(); + } + } + g.setFont(ofont); + } + } + x++; } if (aa.threshold != null) { @@ -1315,6 +1639,52 @@ public class AnnotationPanel extends JPanel implements MouseListener, } } + private int[] getProfileFor(AlignmentAnnotation aa, int column) + { + if (aa.autoCalculated && aa.label.startsWith("Consensus")) + { + if (aa.groupRef != null && aa.groupRef.consensusData != null + && aa.groupRef.isShowSequenceLogo()) + { + return AAFrequency.extractProfile( + aa.groupRef.consensusData[column], aa.groupRef + .getIgnoreGapsConsensus()); + } + // TODO extend annotation row to enable dynamic and static profile data to + // be stored + if (aa.groupRef == null && aa.sequenceRef == null + && av.isShowSequenceLogo()) + { + return AAFrequency.extractProfile(av.hconsensus[column], av + .getIgnoreGapsConsensus()); + } + } + else + { + if (aa.autoCalculated && aa.label.startsWith("StrucConsensus")) + { + if (aa.groupRef != null && aa.groupRef.consensusData != null + && aa.groupRef.isShowSequenceLogo()) + { + //TODO check what happens for group selections + return StructureFrequency.extractProfile( + aa.groupRef.consensusData[column], aa.groupRef + .getIgnoreGapsConsensus()); + } + // TODO extend annotation row to enable dynamic and static profile data + // to + // be stored + if (aa.groupRef == null && aa.sequenceRef == null + && av.isShowSequenceLogo()) + { + return StructureFrequency.extractProfile(av.hStrucConsensus[column], + av.getIgnoreGapsConsensus()); + } + } + } + return null; + } + // used by overview window public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y, int sRes, int eRes)